Identification of Key Candidate Genes Potentially Associated with Lactation Traits in Dairy Cows Using Weighted Gene Co-Expression Network Analysis

Lactation traits are important indicators for evaluating the production performance of dairy cows and the economic efficiency of dairy production. Identifying potential regulatory genes is essential for elucidating the molecular mechanisms underlying lactation and facilitating molecular breeding. This study aimed to identify candidate genes and regulatory pathways potentially associated with lactation traits in dairy cows by integrating transcriptome expression profiles of primary bovine mammary epithelial cells (BMECs) from eight Holstein cows with lactation phenotypic data. A gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA). Co-expression modules associated with lactation traits were identified, and candidate genes were further screened by integrating gene significance, module membership, functional enrichment analysis, random forest analysis, gene-phenotype association analysis, single-gene gene set enrichment analysis (GSEA), ROC curve analysis, and tissue expression profiling. Four co-expression modules, namely MEdarkturquoise, MEsteelblue, MEbrown, and MEskyblue3, were significantly associated with lactation traits (p < 0.05). Genes in these modules were mainly enriched in biological processes and pathways related to ribosome biogenesis, protein translation, the cell cycle, oxidative phosphorylation, and the PI3K-Akt signaling pathway, which may be involved in lactation regulation. Through multi-strategy cross-screening, four candidate genes were ultimately identified. MDM2 was associated with daily milk yield (DYM), RPL37A with total milk solids (TMS), and SLC25A25 and CCNE2 with milk fat percentage (MFP) and fat-to-protein percentage ratio (FPP). Reverse transcription quantitative real-time PCR (RT-qPCR) validation showed that MDM2 and RPL37A were relatively highly expressed in mammary tissue, suggesting that they may be involved in lactation-related biological processes in dairy cows. These findings provide potential candidate regulators and theoretical support for further studies on the molecular mechanisms of lactation traits; however, their functional roles require further validation through in vitro and in vivo experiments.